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====== Installation of ReadSeq 2.1.19 ======

===== Additional libraries =====

Java, already installed.

===== Procedure =====

Here is the procedure to install ReadSeq:

  * ReadSeq is distributed as a JAR archive, ready for execution. Create a folder in ''/home/bioubuntu'' to put the archive in and move this folder to ''/opt/bio/sources''.

  * This folder should belong to ''root'' and its permissions set to ''755''.

<code bash>
% sudo chown -R root:root /opt/bio/sources/readseq-2.1.19-src
% sudo chmod 755 /opt/bio/sources/readseq-2.1.19-src
</code>

  * Once you are in ''/opt/bio/sources/readseq-2.1.19-src'', create two small scripts to make your life easier:
<code bash>
% sudo touch readseq
% sudo touch readseq_gui
</code>

  * For ''readseq'', put the following code:
<code>
#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.19-src/readseq.jar run
</code>

  * For ''readseq_gui'', put the following code:
<code>
#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.19-src/readseq.jar app
</code>


  * You need to make them executable and available to all:
<code bash>
% sudo chmod ugo+x readseq
% sudo ln -s /opt/bio/sources/readseq-2.1.19-src/readseq /usr/local/bin/readseq
% sudo chmod ugo+x readseq_gui
% sudo ln -s /opt/bio/sources/readseq-2.1.19-src/readseq_gui /usr/local/bin/readseq_gui
</code>

  * To add ReadSeq to the Impilo application menu, you need to edit the Xfce4 configuration file:
<code>
% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml
</code>
  * The three things to add are:
    * Item: Launcher
    * Name: Readseq
    * Command: readseq_gui